Synthesis,stereochemistry and antimicrobial studies of novel oxime ethers of aza/diazabicycles

Two series of bicyclic oxime ethers viz, 2,4-diaryl-3-azabicyclo[3.3.1]nonan-9-one O-benzyloximes 13–24 and 2,4,6,8-tetraaryl-3,7-diazabicyclo[3.3.1]nonan-9-one O-benzyloximes 31–36 were synthesized and stereochemistry was established by their spectral (1D and 2D NMR) and crystal studies. Synthesized oxime ethers were screened for their in vitro antimicrobial activity against a set of pathogenic bacteria (Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi, Escherichia coli and Klebsiella pneumoniae) and fungi (Candida albicans, Candida-51, Rhizopus sp., Aspergillus niger and Aspergillus flavus) by twofold serial dilution method, respectively, using Ciprofloxacin and Amphotericin B as standards. Most of the molecules expressed promising antimicrobial profile against the tested pathogens and even a few compounds 16, 21, 22, 33 and 34 were better than standard drugs.     

Antioxidant defense responses: physiological plasticity in higher plants under abiotic constraints

Environmental stresses (salinity, drought, heat/cold, light and other hostile conditions) may trigger in plants oxidative stress, generating the formation of reactive oxygen species (ROS). These species are partially reduced or activated derivatives of oxygen, comprising both free radical and non-radical (H₂O₂) forms, leading to cellular damage, metabolic disorders and senescence processes. In order to overcome oxidative stress, plants have developed two main antioxidants defense mechanisms that can be classified as non-enzymatic and enzymatic systems. The first class (non-enzymatic) consists of small molecules such as vitamin (A, C and E), glutathione, carotenoids and phenolics that can react directly with the ROS by scavenging them. Second class is represented by enzymes among them superoxide dismutase, peroxidase and catalase which have the capacity to eliminate superoxide and hydrogen peroxide. In this review, we have tried to explore the related works, which have revealed the changes in the basic antioxidant metabolism of plants under various abiotic constraints.     

Role of Interferon Gamma Release Assay in Active TB Diagnosis among HIV Infected Individuals

Background

A rapid and specific test is urgently needed for tuberculosis (TB) diagnosis especially among human immunodeficiency virus (HIV) infected individuals. In this study, we assessed the sensitivity of Interferon gamma release assay (IGRA) in active tuberculosis patients who were positive for HIV infection and compared it with that of tuberculin skin test (TST).

Methodology/Principal Findings

A total of 105 HIV-TB patients who were naïve for anti tuberculosis and anti retroviral therapy were included for this study out of which 53 (50%) were culture positive. Of 105 tested, QuantiFERON-TB Gold in-tube (QFT-G) was positive in 65% (95% CI: 56% to 74%), negative in 18% (95% CI: 11% to 25%) and indeterminate in 17% (95% CI: 10% to 24%) of patients. The sensitivity of QFT-G remained similar in pulmonary TB and extra-pulmonary TB patients. The QFT-G positivity was not affected by low CD4 count, but it often gave indeterminate results especially in individuals with CD4 count <200 cells/µl. All of the QFT-G indeterminate patients whose sputum culture were positive, showed ≤0.25 IU/ml of IFN-γ response to phytohemagglutinin (PHA). TST was performed in all the 105 patients and yielded the sensitivity of 31% (95% CI: 40% to 22%). All the TST positives were QFT-G positives. The sensitivity of TST was decreased, when CD4 cell counts declined.

Conclusions/Significance

Our study shows neither QFT-G alone or in combination with TST can be used to exclude the suspicion of active TB disease. However, unlike TST, QFT-G yielded fewer false negative results even in individuals with low CD4 count. The low PHA cut-off point for indeterminate results suggested in this study (≤0.25 IU/ml) may improve the proportion of valid QFT-G results.     

Peroxisome proliferator-activated receptor gamma ligand-mediated apoptosis of hepatocellular carcinoma cells depends upon modulation of PI3Kinase pathway independent of Akt

Background

Ligands of Peroxisome proliferator-activated receptor gamma (PPARγ) can inhibit growth and promote apoptosis in various cancer cells, and thus have the potential to be utilized as anticancer drugs. This potential however, has been seriously challenged by observations that they can lead to tumor promotion in some cancer models, possibly due to activation of different signaling mechanisms in various tumor environments. Elucidation of the specific signaling events that modulate PPARγ ligand-mediated events is thus critical to increase their efficacy. The studies described here were designed to elucidate the signaling pathway(s) that modulate the apoptotic potential of Troglitazone (TRG), an artificial PPARγ ligand in hepatocellular carcinoma (HCC) cells.

Results

Our results indicate that the apoptotic potential of TRG was regulated by the presence or absence of serum in the media. When added in serum-containing media, TRG inhibited proliferation and cyclin D1 expression, but was unable to induce any apoptosis. However, TRG's apoptotic potential was induced significantly when added in serum deficient media, as indicated by increased PARP and Caspase-3 cleavage and results from apoptosis assay. Furthermore, TRG-induced apoptosis in serum deficient media was associated with a dramatic reduction in PI3Kinase downstream target Akt^Ser473 and FoxO1^Thr24/FoxO3a^Thr32 phosphorylation. On the contrary, there was an increase of PI3K-induced Akt^Ser473 and FoxO1^Thr24/FoxO3a^Thr32 phosphorylation involving Pak, when TRG was added in serum-containing media. Pharmacological inhibition of PI3Kinase pathway with LY294002 inhibited Akt^ser473 phosphorylation and sensitized cells towards apoptosis in the presence of serum, indicating the involvement of PI3K in apoptosis resistance. Interestingly, pharmacological inhibition or siRNA-mediated knockdown of Akt or inhibition of Pak was unable to sensitize cells towards TRG-induced apoptosis in the presence of serum. Similarly, TRG was unable to induce apoptosis in the Akt1-KO, Akt1&2-KO MEFs in serum-containing media.

Conclusion

These studies indicate that TRG-induced apoptosis is modulated by PI3K pathway in a novel Akt-independent manner, which might contribute to its tumor promoting effects. Since PI3K activation is linked with various cancers, combination therapy utilizing TRG and PI3K inhibitors has the potential to not only increase the efficacy of TRG as a chemotherapeutic agent but also reduce its off target effects.     

Efficient subfractionation of gram-negative bacteria for proteomics studies

Proteomics studies of pathogenic bacteria are an important basis for biomarker discovery and for the development of antimicrobial drugs and vaccines. Especially where vaccines are concerned, it is of great interest to explore which bacterial factors are exposed on the bacterial cell surface and thus can be directly accessed by the immune system. One crucial step in proteomics studies of bacteria is an efficient subfractionation of their cellular compartments. We set out to compare and improve different protocols for the fractionation of proteins from Gram-negative bacteria into outer membrane, cytoplasmic membrane, periplasmic, and cytosolic fractions, with a focus on the outer membrane. Overall, five methods were compared, three methods for the fast isolation of outer membrane proteins and two methods for the fractionation of each cellular compartment, using Escherichia coli BL21 as a model organism. Proteins from the different fractions were prepared for further mass spectrometric analysis by SDS gel electrophoresis and consecutive in-gel tryptic digestion. Most published subfractionation protocols were not explicitly developed for proteomics applications. Thus, we evaluated not only the separation quality of the five methods but also the suitability of the samples for mass spectrometric analysis. We could obtain high quality mass spectrometry data from one-dimensional SDS-PAGE, which greatly reduces experimental time and sample amount compared to two-dimensional electrophoresis methods. We then applied the most specific fractionation technique to different Gram-negative pathogens, showing that it is efficient in separating the subcellular proteomes independent of the species and that it is capable of producing high-quality proteomics data in electrospray ionization mass spectrometry.     

Laboratory studies on the life cycle of Leydigia acanthocercoides Fisher (1854) (Cladocera: Chydoridae)

The biology of Leydigia acanthocercoides has been studied under laboratory conditions with reference to longevity, instar duration, growth, fecundity and embryonic development at a temperature range of 28–30 °C. It has three preadult and thirteen adult instars. Under the given laboratory conditions this species produces 20 eggs during a life span of 23 days. The number of eggs produced is uniformly constant in all adult instars. The growth rate seems to be exponential in the early phase of the life cycle as in other Cladocera. The general pattern of embryonic development of L. acanthocercoides is similar to those of other tropical cladocerans though differences in the duration of total developmental period have been recorded.Part of Ph.D. thesis.     

Three-dimensional structure of mare diferric lactoferrin at 2.6 A resolution.

Lactoferrin is a monomeric glycoprotein with a molecular mass of approximately 80 kDa. The three-dimensional structure of mare diferric lactoferrin (mlf) has been determined at 2.6 A resolution. The protein crystallizes in the space group P 212121with a=85.2 A, b=99.5 A, c=103.1 A with a solvent content of 55 % (v/v). The structure was solved by the molecular replacement method using human diferric lactoferrin as the model. The structure has been refined using XPLOR to a final R -factor of 0.194 for all data in the 15-2.6 A resolution range. The amino acid sequence of mlf was determined using a cDNA method. The final refined model comprises 5281 protein atoms, 2 Fe3+, 2 CO32-and 112 water molecules. The overall folding of mlf is similar to that of other proteins of the transferrin family. The protein folds into two globular lobes, N and C. The lobes are further divided into two domains, N1 and N2, and C1 and C2. The iron-binding cleft is situated between the domains in each lobe. The N lobe appears to be well ordered and is more stable than the C lobe in mlf unlike in other lactoferrins, where the C lobe is the more stable. The opening of the binding cleft in the N lobe of mlf is narrower than those in other proteins of the transferrin family. This is very unusual and is found only in mare lactoferrin. Apart from certain hydrophobic interactions at the mouth of the cleft, one salt-bridge (Lys301 . . . . . . . . Glu216) crosses between the two walls of the cleft. The two lobes are connected covalently by a three-turn alpha-helix involving residues 334-344. The N lobe displays a highly ordered structure with appreciably low temperature factors. The iron coordination is more symmetrical in the N lobe than in the C lobe. There are only 16 intermolecular hydrogen bonds in the structure of mlf.     

Prediction of MHC class II binding peptides based on an iterative learning model

Background

Prediction of the binding ability of antigen peptides to major histocompatibility complex (MHC) class II molecules is important in vaccine development. The variable length of each binding peptide complicates this prediction. Motivated by a text mining model designed for building a classifier from labeled and unlabeled examples, we have developed an iterative supervised learning model for the prediction of MHC class II binding peptides.

Results

A linear programming (LP) model was employed for the learning task at each iteration, since it is fast and can re-optimize the previous classifier when the training sets are altered. The performance of the new model has been evaluated with benchmark datasets. The outcome demonstrates that the model achieves an accuracy of prediction that is competitive compared to the advanced predictors (the Gibbs sampler and TEPITOPE). The average areas under the ROC curve obtained from one variant of our model are 0.753 and 0.715 for the original and homology reduced benchmark sets, respectively. The corresponding values are respectively 0.744 and 0.673 for the Gibbs sampler and 0.702 and 0.667 for TEPITOPE.

Conclusion

The iterative learning procedure appears to be effective in prediction of MHC class II binders. It offers an alternative approach to this important predictionproblem.